Metabolomics
Metabolomics is a comprehensive quantitative measurement of low molecular weight compounds covering systematically the key metabolites, which represent the whole range of pathways of intermediary metabolism The capability to analyze large arrays of metabolites extracts biochemical information reflecting true functional end-points of overt biological events while other functional genomics technologies such as transcriptomics and proteomics, though highly valuable, merely indicate the potential cause for phenotypic response. Therefore they cannot necessarily predict drug effects, toxicological response or disease states at the phenotype level unless functional validation is added.
Metabolomics bridges this information gap by depicting in particular such functional information since metabolite differences in biological fluids and tissues provide the closest link to the various phenotypic responses. Needless to say, such changes in the biochemical phenotype are of direct interest to pharmaceutical, biotech and health industries once appropriate technology allows the cost-efficient mining and integration of this information.
In general, phenotype is not necessarily predicted by genotype. The gap between genotype and phenotype is spanned by many biochemical reactions each with individual dependencies to various influences, including drugs, nutrition and environmental factors. In this chain of biomolecules from the genes to phenotype, metabolites are the quantifiable molecules with the closest link to phenotype. Many phenotypic and genotypic states, such as a toxic response to a drug or disease prevalence are predicted by differences in the concentrations of functionally relevant metabolites within biological fluids and tissue.
HIV/AIDS
Human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) is a disease of the human immune system caused by infection with human. immunodeficiency virus (HIV). During the initial infection, a person may experience a brief period of influenza-like illness. This is typically followed by a prolonged period without symptoms. As the illness progresses, it interferes more and more with the immune system, making the person much, more likely to get infections, including opportunistic infections and tumors that do not usually affect people who have working immune systems. There is currently no cure or effective HIV vaccine. Treatment consists of antiretroviral therapy (ART), such as high active antiretroviral therapy (HAART) which slows progression of the disease and as of 2010 more than, 6.6 million people were taking them in low and middle income countries.
The United States Center for Disease Control and Prevention created a classification system for HIV, and updated it in 2008. This system classifies HIV infections based on CD4 count and clinical symptoms, and describes the infection in three stages:
Stage 1: CD4 count ≥500 cells/μl and no AIDS defining conditions
Stage 2: CD4 count 200 to 500 cells/μl and no AIDS defining conditions
Stage 3: CD4 count ≤200 cells/μl or AIDS defining conditions
For surveillance purposes, the AIDS diagnosis still stands even if, after treatment, the CD4+ T cell count rises to above 200 per μL of blood or other AIDS-defining illnesses are cured.
However, it is becoming increasingly evident that the CD4 count and viral load do not provide a complete picture of the underlying state of the immune system for HIV patients. Indeed, the extension of life as a consequence of antiretroviral therapies has heralded a new era of non-AIDS-related diseases and incomplete restoration of immune function despite good control of viral loads. Therefore, the identification and incorporation of new predictive markers for HIV diagnosis and classification is of utmost importance.
In sites where antiretroviral drugs have been widely used since the mid-90s, the use of antiretroviral therapy (ART) has changed the natural course of HIV infection, improving the immune system of patients and thus resulting in both reduced incidence of opportunistic infections and increased survival of HIV-infected patients. Recent data shows that in Brazil there has been an increase in survival among patients diagnosed with AIDS, with 63.97% of patients achieving a survival of 108 months. Recently, several efforts have been made in order to understand the pathogenesis of HIV by means of the evaluation of its impact on infected cells, on the discovery of disease biomarkers and the understanding of disease progression through the study of specific subgroups of patients.
Therefore, an urgent need exists in the art for new screening and diagnosing procedures, which can be easily performed and which can provide for more accurate and effective results, as well as for a more reliable prediction of a patient's response to ART.
One promising approach for screening, diagnosing and classifying HIV is the use of biomarkers, such as plasma (or serum) biomarkers (such as antigens and protein patterns). However, they are still far from clinical use.
Pendyala G. and Fox H S. (Proteomic and metabolomic strategies to investigate HIV-associated neurocognitive disorders, Genome Med. 2010; 2(3): 22) describe protein biomarkers for HIV-associated neurocognitive disorders that have been discovered using proteomics, which include complement C3, soluble superoxide dismutase and a prostaglandin synthase. According to the authors, reliable molecular markers could aid in the prediction of development of disease.
Cassol et al. (Plasma metabolomics identifies lipid abnormalities linked to markers of inflammation, microbial translocation, and hepatic function in HIV patients receiving protease inhibitors. BMC Infectious Diseases (2013) 13:203) describe that a 35-metabolite signature mapping to lipid, amino acid, and nucleotide metabolism can distinguish HIV patients with advanced disease on PI-based ART from controls regardless of HCV serostatus. The authors conclude that lipid alterations in HIV patients receiving PI-based ART are linked to markers of inflammation, microbial translocation, and hepatic function, suggesting that therapeutic strategies attenuating dysregulated innate immune activation and hepatic dysfunction may be beneficial for prevention and treatment of metabolic disorders in HIV patients.
Therefore, there is an urgent need in the art to develop new screening and diagnosing techniques suitable for predicting HIV progression, outcome of the disease as well as the patient's therapeutic response to antiretroviral therapy (ART). In particular, new effective biomarkers for HIV screening that can be used individually or in combination with other existing methods are urgently needed.
In view of the above mentioned problems existing in the prior art, the object underlying the present invention is the provision of new biomarkers for assessing HIV, which markers allow for reliable diagnosis of HIV already in an early stage of disease progression. Optimally, the marker should be easily detectable in a biological sample, such as in blood, and its level should be consistently related to the stage of HIV. Moreover, it is an object of the present invention to provide for a method for assessing HIV in a biological sample. Furthermore, the new biomarkers should be suitable for predicting HIV progression, outcome of the disease as well as the patient's therapeutic response to antiretroviral therapy.
In order to solve the objects underlying the present invention the inventors based their investigations on metabolomics as it could give insight in the biochemical changes occurring in the course of HIV development and offer several novel and potentially better biomarkers. The inventors found that a more comprehensive picture of all metabolomics pathways and mechanisms involved in HIV is given when using a panel of metabolites that are altered with progressing HIV rather than employing techniques conventionally performed in the art.